AutoCloner

Multiple sequence alignment - TraesCS2B01G128800

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Download Multiple Sequence Alignment: (Fasta) (Clustal)

BLAST Results

Shown here are the results of a BLAST search against the genome using the input sequence. The pipeline uses this to extract flanking regions for cloning. If the result of the multiple sequence alignment is not as expected, these results could be used for further investigation.

	qseqid	sseqid	percentage.identical	alignment.length	no.mismatch	no.gap.openings	qstart	qend	sstart	send	evalue	bitscore
0	TraesCS2B01G128800	chr2B	100.000	5785	0	0	1	5785	96241339	96235555	0.000000e+00	10683.0
1	TraesCS2B01G128800	chr2B	89.101	2358	224	16	2975	5313	96103754	96101411	0.000000e+00	2900.0
2	TraesCS2B01G128800	chr2B	83.688	1551	219	24	3241	4785	96086123	96084601	0.000000e+00	1432.0
3	TraesCS2B01G128800	chr2B	86.883	1235	101	29	193	1396	96109564	96108360	0.000000e+00	1327.0
4	TraesCS2B01G128800	chr2B	90.338	859	55	11	1385	2230	96106796	96105953	0.000000e+00	1101.0
5	TraesCS2B01G128800	chr2B	88.592	561	57	4	787	1340	96089179	96088619	0.000000e+00	675.0
6	TraesCS2B01G128800	chr2B	88.578	464	45	7	2514	2972	96104320	96103860	1.820000e-154	556.0
7	TraesCS2B01G128800	chr2B	92.000	350	27	1	5324	5672	737235155	737234806	1.870000e-134	490.0
8	TraesCS2B01G128800	chr2B	92.766	235	15	2	2286	2518	96104971	96104737	7.180000e-89	339.0
9	TraesCS2B01G128800	chr2B	91.367	139	4	5	1	133	96109700	96109564	3.560000e-42	183.0
10	TraesCS2B01G128800	chr2B	79.487	117	19	5	5048	5161	561266091	561265977	1.730000e-10	78.7
11	TraesCS2B01G128800	chr2D	91.330	2226	127	22	1	2203	61347917	61345735	0.000000e+00	2981.0
12	TraesCS2B01G128800	chr2D	91.406	1920	150	10	2971	4884	61342356	61340446	0.000000e+00	2617.0
13	TraesCS2B01G128800	chr2D	82.732	1552	236	24	3241	4785	61316837	61315311	0.000000e+00	1352.0
14	TraesCS2B01G128800	chr2D	88.969	553	54	4	787	1332	61318650	61318098	0.000000e+00	676.0
15	TraesCS2B01G128800	chr2D	89.224	464	45	4	2514	2972	61342921	61342458	5.030000e-160	575.0
16	TraesCS2B01G128800	chr2D	92.086	139	8	2	2282	2417	61344920	61344782	5.920000e-45	193.0
17	TraesCS2B01G128800	chr2D	96.522	115	3	1	2404	2518	61343449	61343336	7.650000e-44	189.0
18	TraesCS2B01G128800	chr2D	95.652	46	2	0	2227	2272	61345682	61345637	2.240000e-09	75.0
19	TraesCS2B01G128800	chr2A	91.263	2083	141	23	3193	5242	61959957	61957883	0.000000e+00	2800.0
20	TraesCS2B01G128800	chr2A	89.683	1483	106	17	778	2230	61963078	61961613	0.000000e+00	1847.0
21	TraesCS2B01G128800	chr2A	83.126	1529	214	30	3241	4765	61810032	61808544	0.000000e+00	1354.0
22	TraesCS2B01G128800	chr2A	91.989	699	46	8	2280	2972	61960772	61960078	0.000000e+00	972.0
23	TraesCS2B01G128800	chr2A	89.350	554	52	4	787	1333	61817828	61817275	0.000000e+00	689.0
24	TraesCS2B01G128800	chr2A	89.942	517	37	11	251	754	61963869	61963355	0.000000e+00	652.0
25	TraesCS2B01G128800	chr2A	94.444	162	5	4	1	158	61964890	61964729	4.480000e-61	246.0
26	TraesCS2B01G128800	chr2A	88.696	115	12	1	5672	5785	61863960	61863846	7.820000e-29	139.0
27	TraesCS2B01G128800	chr2A	92.958	71	4	1	176	245	61963979	61963909	1.030000e-17	102.0
28	TraesCS2B01G128800	chr2A	97.826	46	1	0	2227	2272	61961589	61961544	4.810000e-11	80.5
29	TraesCS2B01G128800	chr2A	92.000	50	4	0	1832	1881	569285165	569285214	2.890000e-08	71.3
30	TraesCS2B01G128800	chr6B	91.460	363	28	3	5311	5672	452089134	452089494	4.030000e-136	496.0
31	TraesCS2B01G128800	chr7B	90.608	362	30	3	5314	5672	135534157	135534517	1.460000e-130	477.0
32	TraesCS2B01G128800	chr7B	90.556	360	31	3	5314	5672	599876348	599876705	1.890000e-129	473.0
33	TraesCS2B01G128800	chr7B	89.779	362	31	6	5314	5672	607323096	607322738	5.280000e-125	459.0
34	TraesCS2B01G128800	chr7B	97.143	35	1	0	1852	1886	186973980	186973946	6.260000e-05	60.2
35	TraesCS2B01G128800	chr4B	90.556	360	32	2	5314	5672	15844271	15844629	5.250000e-130	475.0
36	TraesCS2B01G128800	chr4B	90.331	362	29	5	5314	5672	498933401	498933759	2.440000e-128	470.0
37	TraesCS2B01G128800	chr4B	90.305	361	29	5	5314	5672	661616988	661616632	8.780000e-128	468.0
38	TraesCS2B01G128800	chr4A	90.305	361	32	3	5314	5672	650667082	650667441	2.440000e-128	470.0
39	TraesCS2B01G128800	chr1A	82.963	135	20	2	5048	5181	59130345	59130213	1.020000e-22	119.0
40	TraesCS2B01G128800	chr1D	84.483	116	13	2	5674	5784	273897921	273898036	6.130000e-20	110.0
41	TraesCS2B01G128800	chr3B	75.758	231	42	11	5048	5270	711066570	711066346	2.850000e-18	104.0
42	TraesCS2B01G128800	chr3B	75.598	209	37	12	5048	5248	710596339	710596541	2.220000e-14	91.6
43	TraesCS2B01G128800	chr3A	76.842	190	32	11	5048	5230	672591092	672591276	4.770000e-16	97.1
44	TraesCS2B01G128800	chr3D	80.508	118	17	5	5673	5785	554166067	554165951	1.030000e-12	86.1
45	TraesCS2B01G128800	chr3D	80.165	121	15	6	5669	5783	429720933	429720816	1.340000e-11	82.4
46	TraesCS2B01G128800	chr1B	90.164	61	5	1	5726	5785	373257447	373257507	1.730000e-10	78.7
47	TraesCS2B01G128800	chr7A	89.362	47	5	0	1841	1887	520447006	520447052	6.260000e-05	60.2
48	TraesCS2B01G128800	chr5B	97.143	35	0	1	5726	5760	34727316	34727283	2.250000e-04	58.4

These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

	query	scaffold	start	end	length	rev.comp	avg.bitscore	max.bitscore	avg.percent.identical	query.start	query.end	num_hsp	groupid	homo_length
0	TraesCS2B01G128800	chr2B	96235555	96241339	5784	True	10683.000000	10683	100.000000	1	5785	1	chr2B.!!$R1	5784
1	TraesCS2B01G128800	chr2B	96101411	96109700	8289	True	1067.666667	2900	89.838833	1	5313	6	chr2B.!!$R5	5312
2	TraesCS2B01G128800	chr2B	96084601	96089179	4578	True	1053.500000	1432	86.140000	787	4785	2	chr2B.!!$R4	3998
3	TraesCS2B01G128800	chr2D	61340446	61347917	7471	True	1105.000000	2981	92.703333	1	4884	6	chr2D.!!$R2	4883
4	TraesCS2B01G128800	chr2D	61315311	61318650	3339	True	1014.000000	1352	85.850500	787	4785	2	chr2D.!!$R1	3998
5	TraesCS2B01G128800	chr2A	61808544	61810032	1488	True	1354.000000	1354	83.126000	3241	4765	1	chr2A.!!$R1	1524
6	TraesCS2B01G128800	chr2A	61957883	61964890	7007	True	957.071429	2800	92.586429	1	5242	7	chr2A.!!$R4	5241
7	TraesCS2B01G128800	chr2A	61817275	61817828	553	True	689.000000	689	89.350000	787	1333	1	chr2A.!!$R2	546

AutoCloner calculated primer pairs

These primer pairs were selected by Autocloner to minimize primer penalty (calculated by Primer3), whilst remaining within the specified product range where possible.

Download AutoCloner chosen primers as CSV: (Forward) (Reverse)

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
735	1520	0.818040	GGTTGCCGTCAGAAGGTTGT	60.818	55.000	4.13	0.00	0.00	3.32	F
785	1829	1.083806	ATATATGCGCATGCCCGACG	61.084	55.000	32.48	0.00	41.78	5.12	F
2106	4865	1.306148	GTACTAATTTGAGCGCCCCC	58.694	55.000	2.29	0.00	0.00	5.40	F
2211	4971	0.449388	GTGTGCATAGCTGTTCAGCC	59.551	55.000	19.28	6.52	34.90	4.85	F
2973	9110	1.191647	GTAGGAGTTCAAACGTGTGCG	59.808	52.381	0.00	0.00	44.93	5.34	F
3000	9137	1.328680	GTAGAATGTCAGCATGCACCG	59.671	52.381	21.98	8.00	32.93	4.94	F
3228	9365	2.505407	TCACTTGGATATGTCTGGGGTG	59.495	50.000	0.00	0.00	0.00	4.61	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1898	4650	0.679640	TGGCGAACATGATTGGACCC	60.680	55.000	0.00	0.00	0.00	4.46	R
2114	4873	1.083489	TATTGCTTTTCCACGCGGAG	58.917	50.000	12.47	1.64	44.10	4.63	R
3708	9850	0.898789	AGTACACGGTCACCCTCCTG	60.899	60.000	0.00	0.00	0.00	3.86	R
3721	9863	2.349532	GCTTGCCTTCGTTGAAGTACAC	60.350	50.000	5.88	0.00	37.92	2.90	R
4237	10411	1.270518	CGGAGATGAGGCCCAAGTATG	60.271	57.143	0.00	0.00	0.00	2.39	R
4289	10463	5.348997	GTGTTCTATTCCTCTTTGAAGTCCG	59.651	44.000	0.00	0.00	0.00	4.79	R
5128	11316	0.398664	TTAGCTAGTCCAGAGGCCCC	60.399	60.000	0.00	0.00	0.00	5.80	R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)

Show entries

Search:

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
280	1030	9.280174	TGGTTAGTTCAAATCTAAAGTAACTGG	57.720	33.333	10.81	0.00	39.54	4.00
450	1228	6.620678	AGTGTTCAATAAAATTCCGATGTGG	58.379	36.000	0.00	0.00	40.09	4.17
537	1319	4.508124	CGCTATGTGTCTTCTTCCCATAAC	59.492	45.833	0.00	0.00	0.00	1.89
635	1417	6.535508	ACGTTTCTCCTTTACTTATGATCTGC	59.464	38.462	0.00	0.00	0.00	4.26
735	1520	0.818040	GGTTGCCGTCAGAAGGTTGT	60.818	55.000	4.13	0.00	0.00	3.32
760	1550	1.541670	GCAACCTCCGTAAGTTCCACA	60.542	52.381	0.00	0.00	0.00	4.17
761	1551	2.874457	GCAACCTCCGTAAGTTCCACAT	60.874	50.000	0.00	0.00	0.00	3.21
762	1552	3.618019	GCAACCTCCGTAAGTTCCACATA	60.618	47.826	0.00	0.00	0.00	2.29
763	1553	4.766375	CAACCTCCGTAAGTTCCACATAT	58.234	43.478	0.00	0.00	0.00	1.78
764	1554	5.682990	GCAACCTCCGTAAGTTCCACATATA	60.683	44.000	0.00	0.00	0.00	0.86
765	1555	6.522054	CAACCTCCGTAAGTTCCACATATAT	58.478	40.000	0.00	0.00	0.00	0.86
766	1556	7.663827	CAACCTCCGTAAGTTCCACATATATA	58.336	38.462	0.00	0.00	0.00	0.86
767	1557	8.311836	CAACCTCCGTAAGTTCCACATATATAT	58.688	37.037	0.00	0.00	0.00	0.86
785	1829	1.083806	ATATATGCGCATGCCCGACG	61.084	55.000	32.48	0.00	41.78	5.12
873	1924	3.669536	TGAAATGAAGGCGTATGTGACA	58.330	40.909	0.00	0.00	0.00	3.58
930	1981	4.436998	GCGGTGCACTACTCGGCT	62.437	66.667	17.98	0.00	35.79	5.52
966	2017	4.373116	TCCTTGACGCCGGCTGAC	62.373	66.667	26.68	18.04	0.00	3.51
982	2033	1.971167	GACAAGCGGTCATTGGCCA	60.971	57.895	0.00	0.00	46.19	5.36
1017	2068	2.363276	ATGGGACTCGCCACGGTA	60.363	61.111	0.00	0.00	38.95	4.02
1182	2233	2.108514	CCACGTCATGAGCCGCATT	61.109	57.895	0.00	0.00	34.15	3.56
1185	2236	2.466982	CGTCATGAGCCGCATTGCT	61.467	57.895	7.12	0.00	46.37	3.91
1435	4089	8.671921	CATATCTAGTTCAATGTTGTGAAAGCT	58.328	33.333	0.00	0.00	39.18	3.74
1623	4320	2.507886	TCAGGACAGAGAAACCAAACCA	59.492	45.455	0.00	0.00	0.00	3.67
1673	4423	2.288666	GATAAATTCAGCCGCCAGTGA	58.711	47.619	0.00	0.00	0.00	3.41
1762	4512	2.364970	CCAAACCAAACAGATGCCTTCA	59.635	45.455	0.00	0.00	0.00	3.02

Showing 1 to 25 of 414 entries

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Show entries

Search:

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
398	1172	3.696051	TGCATAGAAATGTGGAAGGAAGC	59.304	43.478	0.00	0.00	35.38	3.86
450	1228	3.282374	ATGAGGCCGGGTTGGTTCC	62.282	63.158	2.18	0.00	41.21	3.62
557	1339	5.189736	ACAATCACTATGGTTTAGCTGAGGA	59.810	40.000	0.00	0.00	0.00	3.71
588	1370	7.481642	ACGTATTGACAAACCAAACATTAACA	58.518	30.769	0.00	0.00	0.00	2.41
735	1520	1.477553	ACTTACGGAGGTTGCGGATA	58.522	50.000	0.00	0.00	34.75	2.59
760	1550	6.042777	GTCGGGCATGCGCATATATATATAT	58.957	40.000	31.00	9.12	41.24	0.86
761	1551	5.407502	GTCGGGCATGCGCATATATATATA	58.592	41.667	31.00	4.92	41.24	0.86
762	1552	4.245660	GTCGGGCATGCGCATATATATAT	58.754	43.478	31.00	0.00	41.24	0.86
763	1553	3.649073	GTCGGGCATGCGCATATATATA	58.351	45.455	31.00	4.44	41.24	0.86
764	1554	2.483876	GTCGGGCATGCGCATATATAT	58.516	47.619	31.00	0.00	41.24	0.86
765	1555	1.801025	CGTCGGGCATGCGCATATATA	60.801	52.381	31.00	5.01	41.24	0.86
766	1556	1.083806	CGTCGGGCATGCGCATATAT	61.084	55.000	31.00	0.00	41.24	0.86
767	1557	1.736282	CGTCGGGCATGCGCATATA	60.736	57.895	31.00	12.79	41.24	0.86
774	1564	0.529773	TCTATCAACGTCGGGCATGC	60.530	55.000	9.90	9.90	0.00	4.06
785	1829	9.362539	TCGAAGTTTAATTACACCTCTATCAAC	57.637	33.333	0.00	0.00	0.00	3.18
873	1924	2.352030	CGCCATCAGCACATTTTCTTGT	60.352	45.455	0.00	0.00	44.04	3.16
966	2017	1.080569	GTTGGCCAATGACCGCTTG	60.081	57.895	23.66	0.00	0.00	4.01
977	2028	2.016604	GCCTGATAACATCGTTGGCCA	61.017	52.381	0.00	0.00	37.04	5.36
982	2033	3.470709	CCATCTGCCTGATAACATCGTT	58.529	45.455	0.00	0.00	33.36	3.85
1185	2236	0.181114	CATTCCTTCTGGCGATCCCA	59.819	55.000	3.30	3.30	42.79	4.37
1251	2302	0.619832	AGAGGCCATGGAAGAGCTCA	60.620	55.000	18.40	0.00	0.00	4.26
1623	4320	2.224450	GCCTATACGCCCCTGTATTTGT	60.224	50.000	0.00	0.00	36.48	2.83
1710	4460	2.049063	GCTCGCCCTATACGCAGG	60.049	66.667	0.00	0.00	35.26	4.85
1714	4464	1.658994	TTTTTGGCTCGCCCTATACG	58.341	50.000	5.33	0.00	34.56	3.06
1738	4488	1.416030	GGCATCTGTTTGGTTTGGGTT	59.584	47.619	0.00	0.00	0.00	4.11

Showing 1 to 25 of 385 entries

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Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.